Editing Comparative genomics (section)

==History==
''See also'': [[History of genomics]]

Comparative genomics has a root in the comparison of [[virus]] genomes in the early 1980s.<ref name=koonin/> For example, small [[RNA viruses]] infecting animals ([[picornaviruses]]) and those infecting plants ([[cowpea mosaic virus]]) were compared and turned out to share significant sequence similarity and, in part, the order of their genes.<ref>{{cite journal | vauthors = Argos P, Kamer G, Nicklin MJ, Wimmer E | title = Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families | journal = Nucleic Acids Research | volume = 12 | issue = 18 | pages = 7251–7267 | date = September 1984 | pmid = 6384934 | pmc = 320155 | doi = 10.1093/nar/12.18.7251 }}</ref> In 1986, the first comparative genomic study at a larger scale was published, comparing the genomes of [[varicella-zoster virus]] and [[Epstein-Barr virus]] that contained more than 100 genes each.<ref>{{cite journal | vauthors = McGeoch DJ, Davison AJ | title = DNA sequence of the herpes simplex virus type 1 gene encoding glycoprotein gH, and identification of homologues in the genomes of varicella-zoster virus and Epstein-Barr virus | journal = Nucleic Acids Research | volume = 14 | issue = 10 | pages = 4281–4292 | date = May 1986 | pmid = 3012465 | pmc = 339861 | doi = 10.1093/nar/14.10.4281 }}</ref>

The first complete genome sequence of a cellular organism, that of ''[[Haemophilus influenzae]]'' Rd, was published in 1995.<ref>{{cite journal | vauthors = Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM | title = Whole-genome random sequencing and assembly of Haemophilus influenzae Rd | journal = Science | volume = 269 | issue = 5223 | pages = 496–512 | date = July 1995 | pmid = 7542800 | doi = 10.1126/science.7542800 | bibcode = 1995Sci...269..496F }}</ref> The second genome sequencing paper was of the small parasitic bacterium ''Mycoplasma genitalium'' published in the same year.<ref>{{cite journal | vauthors = Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison CA, Venter JC | title = The minimal gene complement of Mycoplasma genitalium | journal = Science | volume = 270 | issue = 5235 | pages = 397–403 | date = October 1995 | pmid = 7569993 | doi = 10.1126/science.270.5235.397 | s2cid = 29825758 | bibcode = 1995Sci...270..397F }}</ref> Starting from this paper, reports on new genomes inevitably became comparative-genomic studies.<ref name=koonin/>

''Microbial genomes.'' The first high-resolution whole genome comparison system of microbial genomes of 10-15kbp was developed in 1998 by Art Delcher, Simon Kasif and Steven Salzberg and applied to the comparison of entire highly related microbial organisms with their collaborators at the Institute for Genomic Research (TIGR). The system is called [[MUMmer|MUMMER]] and was described in a publication in Nucleic Acids Research in 1999. The system helps researchers to identify large rearrangements, single base mutations, reversals, tandem repeat expansions and other polymorphisms. In bacteria, MUMMER enables the identification of polymorphisms that are responsible for virulence, pathogenicity, and anti-biotic resistance. The system was also applied to the Minimal Organism Project at TIGR and subsequently to many other comparative genomics projects.

''Eukaryote genomes.'' ''[[Saccharomyces cerevisiae]]'', the baker's yeast, was the first [[eukaryote]] to have its complete genome sequence published in 1996.<ref>{{cite journal | vauthors = Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG | title = Life with 6000 genes | journal = Science | volume = 274 | issue = 5287 | pages = 546, 563-546, 567 | date = October 1996 | pmid = 8849441 | doi = 10.1126/science.274.5287.546 | s2cid = 16763139 | bibcode = 1996Sci...274..546G }}</ref> After the publication of the roundworm ''[[Caenorhabditis elegans]]'' genome in 1998<ref name=science.282.5396.2012/> and together with the fruit fly ''[[Drosophila melanogaster]]'' genome in 2000,<ref>{{cite journal | vauthors = Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC | title = The genome sequence of Drosophila melanogaster | journal = Science | volume = 287 | issue = 5461 | pages = 2185–2195 | date = March 2000 | pmid = 10731132 | doi = 10.1126/science.287.5461.2185 | citeseerx = 10.1.1.549.8639 | bibcode = 2000Sci...287.2185. }}</ref> [[Gerald M. Rubin]] and his team published a paper titled "Comparative Genomics of the Eukaryotes", in which they compared the genomes of the [[eukaryotes]] ''D. melanogaster'', ''C. elegans'', and ''S. cerevisiae'', as well as the [[prokaryote]] ''H. influenzae''.<ref>{{cite journal | vauthors = Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S | title = Comparative genomics of the eukaryotes | journal = Science | volume = 287 | issue = 5461 | pages = 2204–2215 | date = March 2000 | pmid = 10731134 | pmc = 2754258 | doi = 10.1126/science.287.5461.2204 | author-link15 = Michael Ashburner | author-link16 = Ewan Birney | bibcode = 2000Sci...287.2204. | author-link1 = Gerald M. Rubin }}</ref> At the same time, [[Bonnie Berger]], [[Eric Lander]], and their team published a paper on whole-genome comparison of human and mouse.<ref>{{cite journal |vauthors=Batzoglou S, Pachter L, Mesirov JP, Berger B, Lander ES |title=Human and mouse gene structure: comparative analysis and application to exon prediction |journal=Genome Research |volume=10 |issue=7 |pages=950–958 |date=July 2000 |pmid=10899144 |pmc=310911 |doi=10.1101/gr.10.7.950 |doi-access=free}}</ref>

With the publication of the large genomes of vertebrates in the 2000s, including [[Human Genome Project|human]], the [[Japanese pufferfish]] ''[[Takifugu rubripes]]'', and [[House mouse|mouse]], precomputed results of large genome comparisons have been released for downloading or for visualization in a [[genome browser]]. Instead of undertaking their own analyses, most biologists can access these large cross-species comparisons and avoid the impracticality caused by the size of the genomes.<ref>{{cite journal | vauthors = Ureta-Vidal A, Ettwiller L, Birney E | title = Comparative genomics: genome-wide analysis in metazoan eukaryotes | journal = Nature Reviews. Genetics | volume = 4 | issue = 4 | pages = 251–262 | date = April 2003 | pmid = 12671656 | doi = 10.1038/nrg1043 | s2cid = 2037634 }}</ref>

[[Next-generation sequencing]] methods, which were first introduced in 2007, have produced an enormous amount of genomic data and have allowed researchers to generate multiple (prokaryotic) draft genome sequences at once. These methods can also quickly uncover [[single-nucleotide polymorphisms]], [[Insertion (genetics)|insertions]] and [[Deletion (genetics)|deletions]] by mapping [[Sequence assembly|unassembled reads]] against a well [[Genome annotation|annotated]] reference genome, and thus provide a list of possible gene differences that may be the basis for any functional variation among strains.<ref name=hu/>